Microbial composition, potential functional roles and genetic novelty in gypsum-rich and hypersaline soils of Monegros and Gallocanta (Spain)

Microbial diversity in polyextreme salt flats and their potential applications

Recent geological, hydrochemical, and mineralogical studies performed on hypersaline salt flats have given insights into similar geo-morphologic features on Mars. These salt-encrusted depressions are widely spread across the Earth, where they are characterized by high salt concentrations, intense UV radiation, high evaporation, and low precipitation. Their surfaces are completely dry in summer; intermittent flooding occurs in winter turning them into transitory hypersaline lakes. Thanks to new approaches such as culture-dependent, culture-independent, and metagenomic-based methods, it is important to study microbial life under polyextreme conditions and understand what lives in these dynamic ecosystems and how they function. Regarding these particular features, new halophilic microorganisms have been isolated from some salt flats and identified as excellent producers of primary and secondary metabolites and granules such as halocins, enzymes, carotenoids, polyhydroxyalkanoates, and exopolysaccharides. Additionally, halophilic microorganisms are implemented in heavy metal bioremediation and hypersaline wastewater treatment. As a result, there is a growing interest in the distribution of halophilic microorganisms around the world that can be looked upon as good models to develop sustainable biotechnological processes for all fields. This review provides insights into diversity, ecology, metabolism, and genomics of halophiles in hypersaline salt flats worldwide as well as their potential uses in biotechnology.

Cold sediment microbial community shifts in response to crude oil water-accommodated fraction with or without dispersant: a microcosm study

In cold environments, the low temperature slows down microbial metabolisms, such as the biodegradation processes of hydrocarbons, which are often stimulated by the addition of dispersants in oil spill disasters. In this study, we investigated the effects of hydrocarbon water-accommodated fraction (WAF) prepared with and without dispersant on benthic microbial communities in a microcosm experiment in which hydrocarbon removal was observed. Both WAFs contained similar polycyclic aromatic hydrocarbon (PAH) content. The microcosm experiment, set up with either pristine or contaminated sediments, was conducted for 21 days at 4 °C under WAF and WAF + dispersant conditions. The behavior of bacterial communities in response to WAF and WAF + dispersant was examined at both DNA and RNA levels, revealing the effect of WAF and WAF + dispersant on the resident and active communities respectively. The contaminated sediment showed less taxa responsive to the addition of both WAF and WAF + dispersant than the pristine sediment, indicating the legacy effect by the presence hydrocarbon-degrading and dispersant-resistant taxa inhabiting the contaminated sediment.

Upside down sulphate dynamics in a saline inland lake

The sulphur cycle has a key role on the fate of nutrients through its several interconnected reactions. Although sulphur cycling in aquatic ecosystems has been thoroughly studied since the early 70's, its characterisation in saline endorheic lakes still deserves further exploration. Gallocanta Lake (NE Spain) is an ephemeral saline inland lake whose main sulphate source is found on the lake bed minerals and leads to dissolved sulphate concentrations higher than those of seawater. An integrative study including geochemical and isotopic characterization of surface water, porewater and sediment has been performed to address how sulphur cycling is constrained by the geological background. In freshwater and marine environments, sulphate concentration decreases with depth are commonly associated with bacterial sulphate reduction (BSR). However, in Gallocanta Lake sulphate concentrations in porewater increase from 60 mM at the water-sediment interface to 230 mM at 25 cm depth. This extreme increase could be caused by dissolution of the sulphate rich mineral epsomite (MgSO₄·7H₂O). Sulphur isotopic data was used to validate this hypothesis and demonstrate the occurrence of BSR near the water-sediment interface. This dynamic prevents methane production and release from the anoxic sediment, which is advantageous in the current context of global warming. These results underline that geological context should be considered in future biogeochemical studies of inland lakes with higher potential availability of electron acceptors in the lake bed compared to the water column.

Vertical organization of microbial communities in Salineta hypersaline wetland, Spain

Microbial communities inhabiting hypersaline wetlands, well adapted to the environmental fluctuations due to flooding and desiccation events, play a key role in the biogeochemical cycles, ensuring ecosystem service. To better understand the ecosystem functioning, we studied soil microbial communities of Salineta wetland (NE Spain) in dry and wet seasons in three different landscape stations representing situations characteristic of ephemeral saline lakes: S1 soil usually submerged, S2 soil intermittently flooded, and S3 soil with halophytes. Microbial community composition was determined according to different redox layers by 16S rRNA gene barcoding. We observed reversed redox gradient, negative at the surface and positive in depth, which was identified by PERMANOVA as the main factor explaining microbial distribution. The Pseudomonadota, Gemmatimonadota, Bacteroidota, Desulfobacterota, and Halobacteriota phyla were dominant in all stations. Linear discriminant analysis effect size (LEfSe) revealed that the upper soil surface layer was characterized by the predominance of operational taxonomic units (OTUs) affiliated to strictly or facultative anaerobic halophilic bacteria and archaea while the subsurface soil layer was dominated by an OTU affiliated to Roseibaca, an aerobic alkali-tolerant bacterium. In addition, the potential functional capabilities, inferred by PICRUSt2 analysis, involved in carbon, nitrogen, and sulfur cycles were similar in all samples, irrespective of the redox stratification, suggesting functional redundancy. Our findings show microbial community changes according to water flooding conditions, which represent useful information for biomonitoring and management of these wetlands whose extreme aridity and salinity conditions are exposed to irreversible changes due to human activities.

Ecological and Metabolic Thresholds in the Bacterial, Protist, and Fungal Microbiome of Ephemeral Saline Lakes (Monegros Desert, Spain)

We studied the 16S and 18S rRNA genes of the bacterial, protist, and fungal microbiomes of 131 samples collected in 14 ephemeral small inland lakes located in the endorheic area of the Monegros Desert (NE Spain). The sampling covered different temporal flooding/desiccation cycles that created natural salinity gradients between 0.1% (w/v) and salt saturation. We aimed to test the hypothesis of a lack of competitive advantage for microorganisms using the "salt-in" strategy in highly fluctuating hypersaline environments where temperature and salinity transitions widely vary within short time periods, as in ephemeral inland lakes. Overall, 5653 bacterial zOTUs and 2658 eukaryal zOTUs were detected heterogeneously distributed with significant variations on taxonomy and general energy-yielding metabolisms and trophic strategies along the gradient. We observed a more diverse bacterial assembly than initially expected at extreme salinities and a lack of dominance of a few "salt-in" organisms. Microbial thresholds were unveiled for these highly fluctuating hypersaline environments with high selective pressures. We conclude that the extremely high dynamism observed in the ephemeral lakes of Monegros may have given a competitive advantage for more versatile ("salt-out") organisms compared to those better adapted to stable high salinities usually more common in solar salterns. Ephemeral inland saline lakes offered a well-suited natural framework for highly detailed evolutionary and ecological studies.

A Methodology for Assessing Groundwater Pollution Hazard by Nitrates from Agricultural Sources: Application to the Gallocanta Groundwater Basin (Spain)

Groundwater pollution by nitrates from agricultural sources is a common environmental issue. In order to support risk analysis, hazard maps are used to classify land uses according to their potential of pollution. The aim of this study is to propose a new hazard index based on nitrogen input and its connection with nitrate concentration in groundwater. The effectiveness of the Nitrogen Input Hazard Index was tested in the Gallocanta Groundwater Basin (Spain), a highly polluted area, declared as a Nitrate Vulnerable Zone. Agricultural data at a plot scale were used to estimate the nitrogen fertilizer requirement of each crop, and the correlation between nitrogen input and nitrate concentration in groundwater was explored. The resulting hazard map allows us to delimit the most hazardous areas, which can be used to implement more accurate nitrate pollution control programs. The index was proven to successfully estimate nitrogen input influence over groundwater nitrate concentration, and to be able to create hazard maps. The criterion used to create categories was empirically based on nitrate concentration thresholds established by the EU Nitrate Directive. The Nitrogen Input Hazard Index may be a useful tool to support risk analyses of agricultural activities in vulnerable areas, where nitrate pollution could endanger human water supply.

Comprehensive assessment of paddy soil quality under land consolidation: a novel perspective of microbiology

Soil quality assessment is an important means to demonstrate how effective land consolidation is. However, the existing assessment system is not sufficient to reflect actual soil quality. So, the purpose of this study is to integrate abiological and biological indicators into a comprehensive assessment to evaluate the paddy soil quality under different land consolidation practices. Soil samples were collected from 35 paddy sites under different land consolidation practices including land merging, land leveling (LL), ditch construction (DC) and application of organic fertilizer (AO). A total of 10 paddy sites were selected under conventional tillage (CT) from non-land consolidation area as a control group in Y county, China. The results indicated that soil organic matter (OM), total nitrogen (TN), available phosphorus, bacterial functional diversity (BFD), bacterial and fungal abundances were significantly improved. Fields under LL, among all the land consolidation practices, might still face the risk of land degradation caused by low TN, OM and microbial diversity. High microbial biomass, BFD and OM were significantly higher in fields under AO in nutrient cycle. According to the results of comprehensive assessment, the samples with severe heavy metal contamination and low microbial diversity were generally concentrated in CT. These results indicated that land consolidation was an efficient technique to improve soil quality and could achieve higher quality of agricultural products.